Inspecting plant growth data

Last compiled: 2019-12-12

1 Purpose

What is the goal of this notebook?

2 Load Data

shoot.data <- read_rds(here("data", "cleaned", "shoots.rds"))
shoot.data

2.1 Data Dictionary

shoot.data contains

• date, the date of the observation
• day, day from first measurement
• field, whether it’s from field A or B
• harvest, did they hareves yesterday?
• plant, plant ID within field. It’s the same plant ever interharvest period
• shoot, shoot ID within plant. These are different shoots each interhavest period
• shoot_id, unique shoot ID in the form of f{field}-h{interhaverst.no}-p{plant}-s{shoot#}
• shoot_height shoot height in cm
• interharvest Which interharvest period? Date listed is the last day of that interharvest period
• interharvest.no Which interharvest period? 1-4 as character, for easier filtering and faceting in plots
• growth difference from the previous day’s shoot_height
• diameter shoot diameter in (UNITS??)
• temp_mean, mean daily temperature in ºC
• temp_max, maximum daily temperature in ºC
• temp_min, minimum daily temperature in ºC
• precip_caas, precip from weather station in mm
• sun_hrs, from weather station
• rh, relative humidity from weather station
• precip_mm, precip from rain gauge

shoot.data2 <- 
  shoot.data %>% 
  mutate(plant_id = paste0(field, plant)) %>% 
  group_by(field, interharvest.no) %>% 
  mutate(day_post = day - first(day),
         temp_mean_lag = lag(temp_mean),
         precip_lag = lag(precip_mm)) %>% 
  ungroup()

3 Exploratory Data Analysis

3.1 Plot growth

Try plotting shoot length over time color = shoot ID, faceted by plant

shoot_grouped <- 
  shoot.data2 %>% 
  group_by(field, interharvest.no) 
df <- group_keys(shoot_grouped)
names <- glue::glue("Field {df$field}, Harvest {df$interharvest.no}")

shoot_growth_list <- group_split(shoot_grouped) %>% set_names(names)
names(shoot_growth_list)

[1] "Field A, Harvest 1" "Field A, Harvest 2" "Field A, Harvest 3" "Field B, Harvest 1"
[5] "Field B, Harvest 2" "Field B, Harvest 3"

plotlist <-
  map2(.x = shoot_growth_list, .y = names(shoot_growth_list), ~{
  ggplot(.x, aes(x = date, y = shoot_height)) +
    geom_line(aes(color = shoot)) +
    facet_wrap(~plant) +
    labs(title = .y) +
    theme(axis.text.x = element_text(angle = 45, hjust = 1))
})

map(plotlist, ggplotly)

$`Field A, Harvest 1`

$`Field A, Harvest 2`

$`Field A, Harvest 3`

$`Field B, Harvest 1`

$`Field B, Harvest 2`

$`Field B, Harvest 3`

NA

There are some obvious measurement errors. Shoots can’t shrink then grow. I checked and these are not data entry errors.

problem.data <-
  tribble(~field, ~interharvest.no, ~plant, ~shoot, ~date, ~adjustment,
          "A",    1,                1,      6,             mdy("6/09/17"), 1,
          "A",    1,                1,      6,             mdy("6/22/17"), 1,
          "A",    1,                1,      6,             mdy("6/23/17"), 1,
          "A",    1,                1,      7,             mdy("6/12/17"), -1,
          "A",    1,                3,      7,             mdy("6/07/17"), -1,
          "A",    1,                3,      4,             mdy("6/07/17"), -1,
          "A",    1,                3,      5,             mdy("6/11/17"), 1,
          "A",    1,                3,      5,             mdy("6/14/17"), 1,
          "A",    1,                5,      2,             mdy("6/11/17"), -1,
          "A",    1,                6,      4,             mdy("6/07/17"), -1,
          "A",    1,                6,      7,             mdy("6/08/17"), -1,
          "A",    1,                8,      7,             mdy("6/10/17"), 1,
          "A",    1,                8,      7,             mdy("6/14/17"), 1,
          "A",    1,                8,      3,             mdy("6/14/17"), -1,
          "A",    1,                8,      3,             mdy("6/17/17"), -1,
          "A",    1,                9,      3,             mdy("6/19/17"), 1,
          "A",    2,                2,      1,             mdy("7/01/17"), -2,
          "A",    2,                3,      6,             mdy("7/02/17"), 1,
          "A",    2,                8,      6,             mdy("7/07/17"), -3,
          "A",    3,                1,      3,             mdy("7/15/17"), -1,
          "A",    3,                2,      3,             mdy("7/14/17"), -1,
          "B",    1,                5,      4,             mdy("6/07/17"), -1,
          "B",    1,                6,      2,             mdy("6/07/17"), 2,
          "B",    2,                1,      5,             mdy("6/16/17"), 1,
          "B",    2,                1,      5,             mdy("7/08/17"), 1,
          "B",    2,                1,      2,             mdy("6/24/17"), -3,
          "B",    2,                1,      3,             mdy("7/06/17"), 3,
          "B",    2,                1,      3,             mdy("7/07/17"), 3,
          "B",    2,                2,      1,             mdy("6/25/17"), -2,
          "B",    2,                4,      1,             mdy("6/20/17"), -2,
          "B",    2,                4,      1,             mdy("7/01/17"), -3,
          "B",    2,                4,      1,             mdy("7/02/17"), -3,
          "B",    2,                4,      1,             mdy("7/05/17"), -4,
          "B",    2,                4,      1,             mdy("7/06/17"), -4,
          "B",    2,                4,      1,             mdy("7/07/17"), -4,
          "B",    2,                4,      1,             mdy("7/08/17"), -4,
          "B",    2,                4,      1,             mdy("7/09/17"), -4,
          "B",    2,                4,      2,             mdy("7/04/17"), 2,
          "B",    2,                4,      2,             mdy("6/30/17"), 2,
          "B",    2,                4,      4,             mdy("6/14/17"), 1,
          "B",    2,                5,      3,             mdy("7/5/17"), 2,
          "B",    2,                6,      4,             mdy("7/11/17"), 2,
          "B",    2,                7,      1,             mdy("7/7/17"), -2,
          "B",    2,                8,      1,             mdy("7/9/17"), 10,
          "B",    2,                10,     3,             mdy("7/04/17"), 15,
          "B",    3,                2,      2,             mdy("7/18/17"), -3,
          "B",    3,                3,      3,             mdy("7/21/17"), 2,
          "B",    3,                5,      3,             mdy("7/21/17"), 2,
          "B",    3,                9,      2,             mdy("7/20/17"), 1
  )

adjust <-
  problem.data %>%
  mutate(shoot_id = paste0("f", field, "-h", interharvest.no, "-p", plant, "-s", shoot)) %>% 
  select(shoot_id, date, adjustment)

shoot.data <-
  left_join(shoot.data, adjust) %>% 
  mutate(shoot_height = ifelse(!is.na(adjustment), shoot_height + adjustment, shoot_height))

Only a couple of these are especially egregious and preliminary analysis shows that “fixing” these errors doesn’t change the results.